Contacts of the strand formed by residues 587 - 593 (chain D) in PDB entry 2DB3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 587 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464D ASP 3.5 3.9 + - - +
465D VAL* 3.4 7.3 - - - -
466D LYS* 2.9 25.2 + - - +
559D LYS* 4.0 10.5 - - - -
580D THR* 4.1 12.3 - - - -
581D GLY* 4.2 4.4 - - - -
586D ASN* 1.3 78.4 - - - +
588D ARG* 1.3 62.3 + - - +
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Residues in contact with ARG 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D VAL* 4.0 4.2 - - - +
466D LYS* 3.4 17.9 - - + +
468D THR* 6.1 0.7 - - - +
484D ILE* 4.3 10.1 + - - +
487D GLU* 4.4 11.7 + - - -
488D GLN* 3.8 31.6 + - - +
559D LYS 3.4 11.9 + - - +
560D HIS* 3.1 55.6 + - + +
561D VAL 3.0 21.5 + - - -
580D THR* 3.8 5.9 + - - -
587D GLY* 1.3 74.6 - - - +
589D ALA* 1.3 62.6 + - - +
590D THR* 4.7 3.2 + - - +
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Residues in contact with ALA 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D VAL* 3.9 9.6 - - + -
466D LYS 2.9 7.6 + - - +
467D GLN* 3.5 6.9 - - + -
468D THR* 3.0 27.3 + - - +
561D VAL* 3.0 15.3 - - + +
573D TYR* 5.3 1.3 - - - +
577D ILE* 3.7 36.6 - - + -
588D ARG* 1.3 76.7 - - - +
590D THR* 1.3 64.5 + - - +
591D SER* 5.1 1.3 - - - +
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Residues in contact with THR 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D THR* 3.3 11.3 + - - +
470D TYR* 3.7 36.8 - - + -
484D ILE* 4.0 15.8 - - + +
560D HIS* 2.7 32.1 + - - -
561D VAL 2.8 6.6 + - - +
562D ILE* 3.1 9.4 - - - +
563D ASN* 2.8 24.3 + - - -
588D ARG* 4.7 4.2 + - - +
589D ALA* 1.3 74.7 + - - +
591D SER* 1.3 66.7 + - - +
592D PHE* 4.2 6.1 - - + -
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Residues in contact with SER 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D THR 2.9 7.1 + - - -
469D ILE* 3.5 22.1 - - - +
470D TYR* 2.8 31.9 + - - +
563D ASN* 2.9 30.0 + - - -
566D MET* 3.8 19.3 - - - -
573D TYR* 3.3 12.6 + - - -
577D ILE* 5.0 0.9 - - - +
589D ALA 5.1 0.9 - - - -
590D THR* 1.3 77.5 + - - +
592D PHE* 1.3 61.8 + - - +
593D PHE 3.8 0.2 - - - -
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Residues in contact with PHE 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470D TYR* 3.7 6.7 - + + -
472D VAL* 4.1 14.8 - - + -
477D LYS* 3.4 45.3 + - + -
480D LYS* 3.6 25.6 - - + -
481D LEU* 3.8 12.6 - - + -
484D ILE* 3.8 25.1 - - + -
562D ILE* 4.4 10.8 - - + -
563D ASN 2.9 11.9 + - - +
564D TYR* 3.4 44.2 - + - +
566D MET* 3.4 20.9 + - - +
590D THR* 4.2 9.4 - - + -
591D SER* 1.3 76.5 - - - +
593D PHE* 1.3 62.1 + - - +
594D ASP 3.7 2.3 + - - -
598D ASP* 3.9 1.7 - - - +
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Residues in contact with PHE 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D ILE* 3.9 16.2 - - + -
470D TYR 2.7 16.8 + - - +
471D GLU* 3.4 1.7 - - - -
472D VAL 2.9 22.8 + - - -
566D MET* 4.2 7.9 - - + -
591D SER 3.7 1.0 + - - -
592D PHE* 1.3 72.7 - - - +
594D ASP* 1.3 56.4 + - - +
595D PRO* 3.3 30.4 - - + +
598D ASP* 3.2 44.2 - - + -
599D ARG* 3.9 8.7 - - + -
601D ILE* 4.4 3.1 - - + -
602D ALA* 4.1 16.6 - - + -
605D LEU* 4.6 8.7 - - + -
619D PHE* 3.7 29.2 - + + -
620D LEU* 3.9 18.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il